Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2025-10-04 12:05 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1055/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.39.1  (landing page)
Stefano de Pretis
Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 Oct 2025)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: devel
git_last_commit: 9163233
git_last_commit_date: 2025-07-22 21:29:21 -0400 (Tue, 22 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for INSPEcT on lconway

To the developers/maintainers of the INSPEcT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/INSPEcT.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: INSPEcT
Version: 1.39.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings INSPEcT_1.39.1.tar.gz
StartedAt: 2025-10-03 22:18:31 -0400 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 22:33:11 -0400 (Fri, 03 Oct 2025)
EllapsedTime: 880.1 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings INSPEcT_1.39.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/INSPEcT.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.39.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘INSPEcT’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   2.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
output_pars: no visible global function definition for ‘plot.new’
plotSingleRNADynamic: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot.new
Consider adding
  importFrom("graphics", "lines", "plot.new")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  INSPEcT-class.Rd: featureNames
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
makeSimDataset                  90.593  0.529  91.699
quantifyExpressionsFromBAMs     38.580  9.465  49.618
modelRates                      43.553  0.236  44.226
INSPEcT_diffsteady-class        33.567  0.346  34.129
rocThresholds                   30.000  0.247  30.499
rocCurve                        29.822  0.227  30.255
makeSimModel                    28.684  0.172  28.995
compareSteady                   28.682  0.172  29.021
plotMA                          27.506  0.150  27.779
quantifyExpressionsFromTrCounts 19.012  0.203  19.371
newINSPEcT                      17.872  0.104  18.073
processingDelay                 15.920  0.089  16.092
inspectFromPCR                   7.499  0.047   7.582
makeOscillatorySimModel          7.234  0.074   7.350
compareSteadyNoNascent           6.440  0.047   6.530
modelRatesNF                     5.482  0.096   5.623
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.


Installation output

INSPEcT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘INSPEcT’ ...
** this is package ‘INSPEcT’ version ‘1.39.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (INSPEcT)

Tests output


Example timings

INSPEcT.Rcheck/INSPEcT-Ex.timings

nameusersystemelapsed
AIC-INSPEcT-method0.2270.0100.238
Extract0.4130.0060.421
INSPEcT_diffsteady-class33.567 0.34634.129
calculateRatePvals0.2430.0040.248
chisqmodel0.1830.0060.192
chisqtest0.2100.0060.218
combine0.4100.0090.427
compareSteady28.682 0.17229.021
compareSteadyNoNascent6.4400.0476.530
convergence0.2050.0060.212
geneClass0.2420.0060.249
inHeatmap0.2270.0070.236
inspectFromPCR7.4990.0477.582
labeledSF0.1980.0050.205
logLik0.2050.0060.214
makeModelRates0.2370.0060.244
makeOscillatorySimModel7.2340.0747.350
makeSimDataset90.593 0.52991.699
makeSimModel28.684 0.17228.995
modelRates43.553 0.23644.226
modelRatesNF5.4820.0965.623
modelSelection0.2030.0050.211
modelingParams0.1950.0050.201
nGenes0.1830.0040.189
nTpts0.2000.0040.211
newINSPEcT17.872 0.10418.073
plotGene0.2400.0050.250
plotMA27.506 0.15027.779
processingDelay15.920 0.08916.092
quantifyExpressionsFromBAMs38.580 9.46549.618
quantifyExpressionsFromTrCounts19.012 0.20319.371
ratePvals0.1870.0030.191
ratesFirstGuess0.1740.0040.180
ratesFirstGuessVar0.1920.0050.200
removeModel0.2800.0030.285
rocCurve29.822 0.22730.255
rocThresholds30.000 0.24730.499
split0.3240.0030.330
tpts0.1980.0030.202
viewConfidenceIntervals0.1970.0060.205
viewModelRates0.1980.0090.216